Through his attorney, Anthony Hopkins, 37, also pleaded not guilty to separate charges of sexual abuse, rape, sodomy and incest.
Prosecutors said the teenage victim in that case is a female relative who is pregnant with his baby. Her disclosure of the alleged sexual abuse led police to find the body in the freezer on July 28.
Mobile County District Judge Charles McKnight set bond at $750,000 on the murder charge in the death of 36-year-old Arletha Hopkins and $10,000 on each of the sex charges. It was not immediately known if Hopkins, father of six of the children, could post bond. He made no comment in court and was returned to jail.
Hopkins maintains his innocence, said defense attorney Jeff Deen. A trial date has not been set.
An autopsy to determine cause of the wife's death has not been completed as investigators waited for the body, which had been contained in a chest-size freezer, to thaw.
The children, ages 3 to 19, were in state custody, but their mother's relatives in Wadley, Ga., were expected to come for them.
At the bond hearing, Assistant District Attorney Ashley Rich described Hopkins as a flight risk and opposed granting bond. Rich told the judge Hopkins had once been absent without leave from the Army in Fort Bragg, N.C. from June 15, 1995 until April 6, 1998 when he was arrested in Saraland, near Mobile. She said he had no steady employment record.
Rich said Hopkins has ties to Alabama, Georgia, Mississippi, Texas and North Carolina.
"He has traveled through many states during his career in the military as well as with his chosen calling. He calls himself a preacher. Based on that, he is a flight risk," Rich told reporters after Tuesday's hearing.
Hopkins, who has lived in Mobile about seven years, had worked four years as a nurse's aide at Searcy Hospital, a state mental facility in north Mobile County, and four years at a shipyard while the Hopkins family performed as a singing group at small churches and Hopkins preached.
Prosecutors told the judge that Hopkins also could face another rape charge involving another teen relative in Jackson, a small town in Clarke County where Hopkins has roots. He was arrested there on July 28 while preaching at a rural revival.
Last week, evangelist Beverly Jackson of Inspirational Tabernacle Church of God In Christ in Jackson, Alabama told CBS affiliate WKRG-TV Anthony Hopkins had just preached about forgiveness when sheriff deputies placed him under arrest.
When Jackson asked police why they were arresting Hopkins, she says they told her, "He murdered his wife." According to Jackson, Hopkins told her that his wife died four years ago while giving birth to their youngest son.
"What in the world is going on? I had no idea that he was even capable of something like this," Jackson told WKRG-TV.
The news also came as a shock to others who say they knew Hopkins as a faithful Christian man who often took the pulpit.
"He appeared to be a real man of God," said Carl Richardson, pastor of the Jackson church. "So, to hear something like this, we have to be careful about who we trust in these days and times."